Load packages

suppressWarnings(suppressMessages({
library(Seurat)
library(magrittr)
library(imager)
library(EBImage)
library(STutility)
library(magrittr)
library(dplyr)
library(DT)
library(kableExtra)
}))

se.cropped <- readRDS("C:/Users/raine/OneDrive/Documents/visium/merge_se_cropped.rds")

Normalization

suppressWarnings(suppressMessages({se.cropped <- se.cropped %>% 
  SCTransform(verbose = F) %>%
  RunPCA(verbose = F) %>%
  RunUMAP(reduction = "pca", dims = 1:20,verbose=F)}))

Idents(se.cropped)="labels"
se.cropped <- RenameIdents(se.cropped,"svze18"="E17.5","svzp2"="P2","svzp12"="P12","svzp22"="P22")
se.cropped$labels <- Idents(se.cropped)
se.cropped@meta.data[["labels"]]=as.character(se.cropped@meta.data[["labels"]])

Visualize only the spots

ST.FeaturePlot(se.cropped, features = c("Sox2", "Pax6"), ncol = 2, grid.ncol = 2, pt.size = 4, show.sb = FALSE)

## Le chargement a nécessité le package : viridis

Visualize normalized gene expression in spots within sections

FeatureOverlay(se.cropped, features = "Sox2",
sampleids = 1:4,
cols = c("light grey", "mistyrose", "darkred"),
pt.size = 3,
add.alpha = TRUE,
ncol = 4, show.sb = FALSE,
pt.alpha = 0.1,label.by = "labels")

Visualize normalized gene expression in spots with section

FeatureOverlay(se.cropped, features = "Lrp2",
sampleids = 1:4,
cols = c("light grey", "mistyrose", "darkred"),
pt.size = 3,
add.alpha = TRUE,
ncol = 4, show.sb = FALSE,
pt.alpha = 0.1,label.by = "labels")

Other visualization parameters

FeatureOverlay(se.cropped, features = "Sox2", 
              sampleids = 1:4,
              cols = c("lightgray", "mistyrose", "red", "darkred", "black"),
              pt.size = 1.5, 
              add.alpha = TRUE,
              ncol = 4,label.by = "labels")